I am sorry you had to go through that, but why would you take it if you knew it was scientifically unsound? I would just say "no, this is scientifically unsound" and refuse to participate. They're going to "detect" whatever they want from my words and punish me accordingly, so I might as well say nothing.

Well, because you don't get a choice, if you don't take it then you don't get what you want (for example, a security clearance or a job), it tends to be a non-negotiable requirement.

You wouldn't get a criminal conviction by refusing to participate, but in other contexts refusal to participate can be (and is) treated the same as failing it.

Ah yes, the good old security clearance polygraph. My friend failed that one 3 times through nervousness. I believe that whole process is just partly to make you nervous and off-balance while they ask you probing questions and partly to signal that you, as an applicant, are willing to ask "how high?" when the government says jump. I did a few clearance processes when I was in the military, ultimately got a TS-SCI, but never took a polygraph; I think because I had a clean-as-a-sheet record since I joined the military a week after my 18th birthday.

It's a compliance test.

If you'll take a polygraph (or engage in any other witchcraft ritual) then you're probably malleable enough to do other dumb things against your better judgement.

In other words you'll act dishonestly to please others or advance yourself. That is to say - it really is a lie detector, just one for seeing how well you can lie to yourself.